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Luna HGC, Imasa MS, Juat N, Hernandez KV, Sayo TM, Cristal-Luna G, Asur-Galang SM, Bellengan M, Duga KJ, Buenaobra BB, De Los Santos MI, Medina D, Samo J, Literal VM, Sy-Naval S. NKX2‑1 copy number alterations are associated with oncogenic, immunological and prognostic remodeling in non‑small cell lung cancer. Oncol Lett 2024; 28:303. [PMID: 38774453 PMCID: PMC11106692 DOI: 10.3892/ol.2024.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/05/2023] [Indexed: 05/24/2024] Open
Abstract
NK2 homeobox 1 (NKX2-1) copy number alterations (CNAs) are frequently observed in lung cancer. However, little is known about the complete landscape of focal alterations in NKX2-1 copy number (CN), their clinical significance and their therapeutic implications in non-small cell lung cancer (NSCLC). The correlations between NKX2-1 expression and EGFR driver mutations and programmed death ligand 1 (PD-L1) co-expression were studied using immunohistochemistry and PCR from the tumors of recruited Filipino patients (n=45). Clinical features of NSCLC with NKX2-1 CNAs were resolved at the tumor and clonal levels using the molecular profiles of patients with lung adenocarcinoma and lung squamous cell carcinoma from The Cancer Genome Atlas (n=1,130), and deconvoluted single-cell RNA-seq data from the Bivona project (n=1,654), respectively. Despite a significant and positive correlation between expression and CN (r=0.264; P<0.001), NKX2-1 CNAs exerted a stronger influence on the combined EGFR and PD-L1 status of NSCLC tumors than expression. NKX2-1 CN gain was prognostic of favorable survival (P=0.018) and a better response to targeted therapy. NKX2-1 CN loss predicted a worse survival (P=0.041). Mutational architecture in the Y-chromosome differentiated the two prognostic groups. There were 19,941 synonymous mutations and 1,408 genome-wide CN perturbations associated with NKX2-1 CNAs. Tumors with NKX2-1 CN gain expressed lymphocyte markers more heterogeneously than those with CN loss. Higher expression of tumor-infiltrating lymphocyte gene signatures in CN gain was prognostic of longer disease-free survival (P=0.005). Tumors with NKX2-1 CN gain had higher B-cell (P<0.001) and total T-cell estimates (P=0.003). NKX2-1 CN loss was associated with immunologically colder tumors due to higher M2 macrophage infiltrates (P=0.011) and higher expression of immune checkpoint proteins, CD274 (P=0.025), VTCN1 (P<0.001) and LGALS9 (P=0.002). In conclusion, NKX2-1 CNAs are associated with tumors that exhibit clinically diverse characteristics, and with unique oncogenic, immunological and prognostic signatures.
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Affiliation(s)
- Herdee Gloriane C. Luna
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Marcelo Severino Imasa
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| | - Necy Juat
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Katherine V. Hernandez
- Department of Internal Medicine, Section of Oncology, East Avenue Medical Center, Quezon City, Metro Manila 1100, Philippines
| | - Treah May Sayo
- Department of Pathology and Laboratory Medicine, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
| | - Gloria Cristal-Luna
- Department of Internal Medicine, Section of Medical Oncology, National Kidney and Transplant Institute, Quezon City, Metro Manila 1101, Philippines
| | - Sheena Marie Asur-Galang
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Mirasol Bellengan
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Kent John Duga
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Bien Brian Buenaobra
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Marvin I. De Los Santos
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
- Globetek Science Foundation Inc., Makati, Metro Manila 1203, Philippines
| | - Daniel Medina
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Jamirah Samo
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Venus Minerva Literal
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig, Metro Manila 1631, Philippines
| | - Sullian Sy-Naval
- Department of Medical Oncology, Lung Center of The Philippines, Quezon City, Metro Manila 1100, Philippines
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Berlanga-Acosta J, Arteaga-Hernandez E, Garcia-Ojalvo A, Duvergel-Calderin D, Rodriguez-Touseiro M, Lopez-Marin L, Suarez-Alba J, Fuentes-Morales D, Mendoza-Fuentes O, Fernández-Puentes S, Nuñez-Figueredo Y, Guillen-Nieto G. Carcinogenic effect of human tumor-derived cell-free filtrates in nude mice. Front Mol Biosci 2024; 11:1361377. [PMID: 38698774 PMCID: PMC11063718 DOI: 10.3389/fmolb.2024.1361377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/18/2024] [Indexed: 05/05/2024] Open
Abstract
Cancer remains a worldwide cause of morbidity and mortality. Investigational research efforts have included the administration of tumor-derived extracts to healthy animals. Having previously demonstrated that the administration of non-transmissible, human cancer-derived homogenates induced malignant tumors in mice, here, we examined the consequences of administering 50 or 100 µg of protein of crude homogenates from mammary carcinoma, pancreatic adenocarcinoma, and melanoma samples in 6 inoculations per week during 2 months. The concurrent control mice received homogenates of healthy donor-skin cosmetic surgery fragments. Mammary carcinoma homogenate administration did not provoke the deterioration or mortality of the animals. Multiple foci of lung adenocarcinomas with a broad expression of malignity histomarkers coexisting with small cell-like carcinomas were found. Disseminated cells, positive to classic epithelial markers, were detected in lymphoid nodes. The administration of pancreatic tumor and melanoma homogenates progressively deteriorated animal health. Pancreatic tumor induced poorly differentiated lung adenocarcinomas and pancreatic islet hyperplasia. Melanoma affected lungs with solid pseudopapillary adenocarcinomas. Giant atypical hepatocytes were also observed. The kidney exhibited dispersed foci of neoplastic cells within a desmoplastic matrix. Nuclear overlapping with hyperchromatic nuclei, mitotic figures, and prominent nuclear atypia was identified in epidermal cells. None of these changes were ever detected in the control mice. Furthermore, the incubation of zebrafish embryos with breast tumor homogenates induced the expression of c-Myc and HER-2 as tumor markers, contrasting to embryos exposed to healthy tissue-derived material. This study confirms and extends our hypothesis that tumor homogenates contain and may act as vectors for "malignancy drivers," which ultimately implement a carcinogenesis process in otherwise healthy mice.
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Affiliation(s)
- Jorge Berlanga-Acosta
- Center for Genetic Engineering and Biotechnology, Biomedical Research Direction, Havana, Cuba
| | | | - Ariana Garcia-Ojalvo
- Center for Genetic Engineering and Biotechnology, Biomedical Research Direction, Havana, Cuba
| | | | | | - Laura Lopez-Marin
- Department of Pathology, Institute for Arteriosclerosis Research, Institute of Nephrology “Dr. Abelardo Buch”, Havana, Cuba
| | - Jose Suarez-Alba
- Center for Genetic Engineering and Biotechnology, Biomedical Research Direction, Havana, Cuba
| | | | - Osmany Mendoza-Fuentes
- Center for Genetic Engineering and Biotechnology, Biomedical Research Direction, Havana, Cuba
| | | | | | - Gerardo Guillen-Nieto
- Center for Genetic Engineering and Biotechnology, Biomedical Research Direction, Havana, Cuba
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Vescio M, Bulloni M, Pelosi G, Pattini L. Lack of imbalance between the master regulators TTF1/NKX2-1 and ΔNp63/p40 implies adverse prognosis in non-small cell lung cancer. Sci Rep 2024; 14:2467. [PMID: 38291083 PMCID: PMC10827720 DOI: 10.1038/s41598-024-52776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
The transcription factors TTF1/NKX2-1 and ΔNp63/p40 are the counterposed molecular markers associated with the main Non-Small Cell Lung Cancer subtypes: TTF1 for adenocarcinoma, p40 for squamous cell carcinoma. Although they generally display a mutually exclusive expression, some exceptions exist simultaneously lacking or (very rarely) expressing both markers, either pattern being associated to poor prognosis. Hence, we quantitatively analyzed the relationship between their coordinated activity and prognosis. By analyzing the respective downstream transcriptional programs of the two genes, we defined a simple quantitative index summarizing the amount of mutual exclusivity between their activities, called Mean Absolute Activity (MAA). Systematic analysis of the MAA index in a dataset of 1018 NSCLC samples replicated on a validation dataset of 275 showed that the loss of imbalance between TTF-1 and p40 corresponds to a steady, progressive reduction in both overall and recurrence-free survival. Coherently, samples correspondent to more balanced activities were enriched for pathways related to increased malignancy and invasiveness. Importantly, multivariate analysis showed that the prognostic significance of the proposed index MAA is independent of other clinical variables including stage, sex, age and smoke exposure. These results hold irrespectively of tumor morphology across NSCLC subtypes, providing a unifying description of different expression patterns.
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Affiliation(s)
- Martina Vescio
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
- CardioTech, IRCCS Centro Cardiologico Monzino, Milan, Italy
| | - Matteo Bulloni
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Inter-Hospital Pathology Division, IRCCS MultiMedica, Milan, Italy
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy.
- CardioTech, IRCCS Centro Cardiologico Monzino, Milan, Italy.
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